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- PDB-4uxz: Structure of delta7-DgkA-syn in 7.9 MAG to 2.18 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4uxz
TitleStructure of delta7-DgkA-syn in 7.9 MAG to 2.18 angstrom resolution
ComponentsDIACYLGLYCEROL KINASE-DELTA 7
KeywordsTRANSFERASE / DIACYLGLYEROL KINASE / IN MESO CRYSTALLIZATION / LIPID CUBIC PHASE / LIPIDIC CUBIC PHASE / LIPID MESOPHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / MONOACYLGLYCEROL
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #3610 / DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / ACETATE ION / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLi, D. / Howe, N. / Caffrey, M.
CitationJournal: Nat.Commun. / Year: 2015
Title: Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.
Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / ...Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / Weierstall, U. / Zatsepin, N.A. / Cherezov, V. / Liu, W. / Bandaru, S. / English, N.J. / Gati, C. / Barty, A. / Yefanov, O. / Chapman, H.N. / Diederichs, K. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Marvin Seibert, M. / Caffrey, M.
History
DepositionAug 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIACYLGLYCEROL KINASE-DELTA 7
B: DIACYLGLYCEROL KINASE-DELTA 7
C: DIACYLGLYCEROL KINASE-DELTA 7
D: DIACYLGLYCEROL KINASE-DELTA 7
E: DIACYLGLYCEROL KINASE-DELTA 7
F: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,15420
Polymers85,2276
Non-polymers3,92714
Water2,360131
1
A: DIACYLGLYCEROL KINASE-DELTA 7
B: DIACYLGLYCEROL KINASE-DELTA 7
C: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,57012
Polymers42,6133
Non-polymers2,9569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-53.5 kcal/mol
Surface area19880 Å2
MethodPQS
2
D: DIACYLGLYCEROL KINASE-DELTA 7
E: DIACYLGLYCEROL KINASE-DELTA 7
F: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5848
Polymers42,6133
Non-polymers9715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-42.8 kcal/mol
Surface area18420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.020, 91.310, 143.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
DIACYLGLYCEROL KINASE-DELTA 7


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PTRCHISB-DGKA-DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 6 types, 145 molecules

#2: Chemical
ChemComp-79N / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H36O4
#3: Chemical
ChemComp-79M / (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / [(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C19H36O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN ...THE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS SEVEN MUTATIONS. THEY ARE A41C, C46A, I53V, I70L, M96L, V107D AND C113A.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 ...Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03315
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.18→75.02 Å / Num. obs: 51820 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 42.36 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.7 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZE3

3ze3


Resolution: 2.18→57.965 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.15 / Stereochemistry target values: ML
Details: THERE ARE SIX NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2348 2556 5 %
Rwork0.2003 --
obs0.202 51436 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.07 Å2
Refinement stepCycle: LAST / Resolution: 2.18→57.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 271 131 5029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145229
X-RAY DIFFRACTIONf_angle_d0.8967085
X-RAY DIFFRACTIONf_dihedral_angle_d13.8771942
X-RAY DIFFRACTIONf_chiral_restr0.058851
X-RAY DIFFRACTIONf_plane_restr0.003860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.22190.36911210.31132642X-RAY DIFFRACTION96
2.2219-2.26730.32491430.30412507X-RAY DIFFRACTION93
2.2673-2.31660.29241480.25082646X-RAY DIFFRACTION98
2.3166-2.37050.25581490.22442651X-RAY DIFFRACTION99
2.3705-2.42980.27451360.20932700X-RAY DIFFRACTION98
2.4298-2.49550.27521300.20712709X-RAY DIFFRACTION98
2.4955-2.56890.24131220.19972716X-RAY DIFFRACTION99
2.5689-2.65180.21961550.17662685X-RAY DIFFRACTION99
2.6518-2.74660.25381330.17462749X-RAY DIFFRACTION99
2.7466-2.85650.19191350.17792720X-RAY DIFFRACTION99
2.8565-2.98650.23571400.17682743X-RAY DIFFRACTION99
2.9865-3.1440.22761610.17682717X-RAY DIFFRACTION99
3.144-3.3410.2341480.19232731X-RAY DIFFRACTION100
3.341-3.59890.21331480.19012763X-RAY DIFFRACTION100
3.5989-3.9610.21951520.18792744X-RAY DIFFRACTION98
3.961-4.53390.20121500.16542761X-RAY DIFFRACTION99
4.5339-5.71150.2431380.22122809X-RAY DIFFRACTION99
5.7115-57.98560.24821470.22912887X-RAY DIFFRACTION97

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